The first formalised definition of a virus species was developed by Marc van Regenmortel and colleagues from the ICTV
(Van Regenmortel et al., 1991):
“A virus species is a polythetic class of viruses that constitute a replicating lineage and occupy a particular ecological niche.”
The species definition for viruses was revised by the ICTV in 2012 as follows:
“A virus species is a monophyletic group of viruses whose properties can be distinguished from those of other species by multiple criteria.”
Features of phenotypic and genomics-based species assignments.
1. Phenotypic assignment：
Provides a biologically and clinically relevant division of viruses；
Species names are typically descriptive and informative；
Variable association with genetic divergence between and within species members；
Assignments may conflict with evolutionary relationships；
Cannot be applied to viruses without information of biological properties (eg., those derived from metagenomic datasets).
2. Genomics-based assignment
Assignments approximate to evolutionary relationships between and within species;
Species names are often serially numbered without any indication of virus properties;
Species may contain viruses with different biological or clinical attributes;
Sequence divergence threshold used species differentiation are variable between virus groups and often arbitrary;
Can be readily applied to viruses with both known and unknown (eg., from metagenomic data) phenotypes.
From ENCYCLOPEDIA OF VIROLOGY FOURTH EDITION by Dennis H. Bamford & Mark Zuckerman.
Viral Isolates, Strains, and Serotypes
The term virus isolate refers to any particular virus culture that is being studied and it is thus simply an instance of a given virus.
Strain: Different lines or isolates of the same virus (e.g., from different geographical locations or patients)
A viral strain is a biological variant of a virus that is recognizable because it possesses some unique phenotypic properties that remain stable under natural conditions. Characteristics that allow strains to be recognized include (1) biological properties such as a particular disease symptom or a particular host, (2) chemical or antigenic properties, and (3) the genome sequence when it is known to be correlated with a unique phenotypic character. If the only difference between a ‘wild type’ virus taken as reference and a particular variant is a small difference in genome sequence, such a variant or mutant is not given the status of a separate strain in the absence of a distinct
phenotypic characteristic.
Strains that possess unique, stable antigenic properties are called serotypes. Serotypes necessarily also possess unique structural, chemical, and genome sequence properties that are related to the differences in antigenicity. Serotypes constitute stable replicating lineages which allow them to remain distinct over time. The infectivity of individual serotypes of animal viruses can be neutralized only by their own specific antibodies and not by antibodies directed to other serotypes. This inablility of serotype-specific antibodies to cross-neutralize other serotypes is important in the case of animal viruses that are submitted to the immunological pressure of their hosts.
from Desk Encyclopedia of GENERAL VIROLOGY by Dr BRIAN W J MAHY & Dr MARC H V VAN REGENMORTEL.
Serotype
A strain of a virus or micro-organism distinguished by its antigens.
A virus type as defined on the basis of neutralizing antibodies.
An isolate or group of isolates that are distinguished from biologically related isolates by reaction (or lack of reaction) with key serological reagents such as defined polyclonal antisera or monoclonal antibodies.
A serotype is defined as either exhibiting no cross-reaction with others or showing a homologous/heterologous titer ratio of greater than 16 (in both directions).
Hyperendemicity：the co-circulation of multiple virus serotypes in the same population.
What is wild type?
Terminology can be confusing. Virologists often use terms such as “strains,” “variants,” and “mutants” to designate a virus that differs in some heritable way from a parental or wild-type virus. In conventional usage, the wild type is defined as the original (often laboratory-adapted) virus from which mutants are selected and which is used as the basis for comparison. A wild-type virus may not be identical to a virus isolated from nature.
In fact, the genome of a wild-type virus may include numerous mutations accumulated during propagation in the laboratory. For example, the genome of the first isolate of poliovirus obtained in 1909 undoubtedly is very different from that of the virus we call wild type today. We distinguish carefully between laboratory wild types and new virus isolates from the natural host. The latter are called field isolates or clinical isolates.
Type: Different serotypes of the same virus (e.g., various antibody neutralization phenotypes).
Variant: A virus whose phenotype differs from the original wild-type strain but the genetic basis for the difference is not known.
Some neutralizing antibodies define type-specific antigens on the virus particle. For example, the three serotypes of poliovirus are distinguished on the basis of neutralization tests: type 1 poliovirus is neutralized by antibodies to type 1 virus but not by antibodies to type 2 or type 3 poliovirus, and so forth. The results of neutralization tests were once used for virus classification, a process now accomplished largely by comparing viral genome sequences. Nevertheless, the detection of antiviral antibodies in animal sera is still extremely important for identifying infected hosts. These antibodies may also be used to map the three-dimensional structure of neutralization antigenic sites on the virus particle.
from Principles of virology, 4th by Flint, S. Jane et al.
